MolNFT v1 · #116186 · protein
Moa-Z-vad-fmk complex, direct orientation
5D61 · Agglutinin: “Moa-Z-vad-fmk complex, direct orientation”. X-ray diffraction, 8 ligands (PHQ, GLA, FUC), 1 pocket (best druggability 0.51). MolNFT v1 #116186 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5D61
- Type
- protein
- Length
- 295 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agglutinin; Z-vad-fmk
- UniProt
- Q8X123
- Ligands
- PHQ, GLA, FUC, GAL, CA, NA, CF0, CL
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agglutinin | protein | 292 | 19% helix, 38% strand | Q8X123 |
| L | Z-vad-fmk | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · chains A, L
- GLA · alpha-D-galactopyranose · sugar · 5 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- CA · Calcium ion · metal · 2 copies · chains A, L
- NA · Sodium ion · metal · chains A
- CF0 · Fluoromethane · ion · chains A, L
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.51 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–L · 200 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5D61 · MOA-Z-VAD-fmk complex, direct orientation · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8X123
- Elsewhere: RCSB PDB 5D61 · PDBe 5D61 · UniProt Q8X123
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